Contacts of the strand formed by residues 230 - 241 (chain A) in PDB entry 1BMA
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A VAL* 3.7 22.9 - - + +
151A ARG* 5.6 0.2 - - - -
152A THR* 3.5 16.5 + - - -
194A GLY* 3.0 37.9 + - - +
195A VAL* 4.0 15.2 + - - +
196A ARG 4.9 0.9 - - - -
197A SER* 3.4 16.2 - - - +
228A GLY 3.6 0.2 - - - -
229A CYS* 1.3 69.1 - - - +
231A VAL* 1.3 64.8 + - - +
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Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A GLY* 3.9 7.1 - - - +
194A GLY* 4.0 3.5 - - - +
225A SER* 4.6 5.4 - - - +
227A LEU* 4.4 14.1 - - + +
228A GLY* 3.5 36.8 - - - +
229A CYS 3.4 4.2 + - - +
230A ASN* 1.3 79.9 - - - +
232A THR* 1.3 77.9 + - - +
233A ARG 3.3 0.5 + - - -
234A LYS* 3.0 44.9 + - + +
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Residues in contact with THR 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A GLY 3.4 10.5 - - - +
193A ASP 3.7 5.9 + - - +
194A GLY* 3.5 18.5 - - - +
231A VAL* 1.3 81.9 - - - +
233A ARG* 1.3 98.3 + - + +
234A LYS* 3.2 3.1 + - - +
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Residues in contact with ARG 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A SER* 3.5 29.2 - - - +
178A TYR* 3.2 62.9 + - + +
192A GLY 3.0 13.6 + - - +
232A THR* 1.3 94.9 - - + +
234A LYS* 1.3 62.5 + - - +
235A PRO* 3.3 8.1 - - - +
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Residues in contact with LYS 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A SER 4.4 5.7 + - - -
178A TYR 2.9 24.0 + - - +
179A TRP* 3.7 44.9 - - + +
192A GLY* 4.4 0.5 - - - -
224A VAL* 5.8 0.9 - - - +
225A SER* 4.2 17.1 + - - +
227A LEU* 5.6 6.7 - - + -
229A CYS 4.7 9.4 - - - +
231A VAL* 3.0 42.0 + - + +
232A THR 4.3 1.5 + - - +
233A ARG* 1.3 81.8 + - - +
235A PRO* 1.3 69.4 - - - +
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Residues in contact with PRO 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A VAL* 4.2 7.6 - - + -
173A CYS* 3.8 26.7 - - - -
178A TYR* 3.8 15.0 - - + -
179A TRP* 3.0 25.0 + - + +
189A CYS* 4.0 3.4 - - + -
190A ALA 3.3 21.1 - - - +
191A GLY 3.6 14.1 - - - +
192A GLY* 3.6 14.1 - - - +
224A VAL* 5.2 0.9 - - - -
233A ARG 3.3 9.4 - - - +
234A LYS* 1.3 95.0 - - - +
236A THR* 1.3 64.1 + - - +
237A VAL* 3.6 1.7 + - - +
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Residues in contact with THR 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU* 4.1 2.8 - - - +
189A CYS* 3.4 3.6 - - - -
190A ALA 2.9 34.3 + - - -
191A GLY* 5.8 0.2 - - - -
192A GLY 4.7 0.8 - - - +
197A SER* 3.5 14.1 - - - -
198A GLY* 3.0 28.6 + - - +
221A THR* 4.0 20.2 - - + -
223A PHE 4.0 4.5 - - - +
224A VAL* 4.0 19.5 - - + +
229A CYS 6.1 0.2 - - - -
234A LYS 3.7 0.6 + - - -
235A PRO* 1.3 71.4 - - - +
237A VAL* 1.4 61.3 + - - +
238A PHE* 3.4 31.2 - - + -
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Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A TRP* 3.5 32.5 - - + +
183A VAL* 4.1 8.7 - - + -
187A MET* 3.7 28.0 - - + -
188A VAL 3.6 5.2 - - - +
189A CYS* 4.6 4.7 - - - -
221A THR* 4.2 0.5 - - - -
222A SER* 2.9 29.3 + - - -
223A PHE* 2.9 63.5 + - + +
235A PRO 3.7 0.9 - - - +
236A THR* 1.4 77.2 - - - +
238A PHE* 1.4 59.4 + - - +
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Residues in contact with PHE 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ILE* 3.9 15.7 - - + -
165A LEU* 4.0 2.5 - - + -
187A MET* 3.1 11.0 - - - +
188A VAL* 2.8 46.2 + - + +
190A ALA* 3.8 17.0 - - + -
207A LEU* 3.8 42.2 - - + -
219A GLY* 3.8 15.0 - - - -
220A VAL 3.3 7.9 - - - +
221A THR* 3.2 41.3 - - + -
222A SER* 4.2 3.6 - - - +
236A THR* 3.4 39.5 - - + -
237A VAL* 1.4 74.6 - - - +
239A THR* 1.3 59.1 + - - +
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Residues in contact with THR 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A GLY* 6.1 0.3 - - - -
107A TYR 5.3 0.7 - - - +
108A ASP* 2.8 44.8 + - - +
109A ILE* 4.1 14.4 - - + -
186A SER 4.1 4.3 - - - +
187A MET* 4.6 3.4 - - - +
219A GLY* 3.3 5.0 - - - -
220A VAL* 2.9 36.4 + - + -
222A SER* 4.1 5.0 - - - -
238A PHE* 1.3 70.4 - - - +
240A ARG* 1.3 61.7 + - - +
241A VAL* 3.2 4.3 + - - +
244A TYR* 3.4 35.4 - - + +
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Residues in contact with ARG 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A GLY* 4.4 0.6 - - - -
134A THR 4.1 3.4 - - - +
135A ILE* 3.4 31.4 - - - +
185A ASN* 3.1 33.7 + - - -
186A SER* 2.9 25.9 + - - +
187A MET 3.9 2.5 - - - +
188A VAL* 3.7 28.3 - - + -
218A HIS* 3.7 7.0 - - - +
238A PHE 3.5 1.4 + - - -
239A THR* 1.3 67.9 - - - +
241A VAL* 1.3 64.7 + - - +
242A SER* 2.8 37.2 + - - +
243A ALA* 3.1 28.6 + - - +
244A TYR* 3.1 15.4 - - - -
290A SO4 2.8 41.4 + - - -
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Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A MET* 3.9 15.9 - - + -
109A ILE* 5.2 2.9 - - + -
129A LEU* 3.9 21.8 - - + -
130A PRO* 4.0 7.2 - - + -
217A VAL 3.7 22.4 - - - +
218A HIS* 3.1 22.1 + - - +
219A GLY 3.9 4.7 - - - +
220A VAL* 3.8 28.5 - - + -
239A THR* 4.1 1.1 - - - +
240A ARG* 1.3 70.2 - - - +
242A SER* 1.3 57.5 + - - +
244A TYR* 2.9 27.6 + - - +
245A ILE* 3.6 14.9 - - + +
248A ILE* 4.6 4.0 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il